Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules

Area of Science:

• Biophysics
• Structural Biology
• X-ray Science

Background:

• X-ray free-electron lasers (XFELs) provide ultra-bright femtosecond X-ray pulses for advanced biomolecular imaging.
• Noncrystalline biomolecular samples present unique experimental and data processing challenges compared to traditional crystallography.

Purpose of the Study:

• To introduce Skopi, a novel simulation package designed for XFEL experiments.
• To facilitate the generation of diverse diffraction image types for algorithm development and feasibility studies.

Main Methods:

• Skopi simulates single-hit diffraction images for reconstruction algorithms.
• It generates multi-hit images for machine learning classifier training.
• Skopi also produces images for fluctuation X-ray scattering and holographic reconstruction.

Main Results:

• The package supports the creation of labeled data for machine learning.
• It enables simulations for various noncrystalline diffraction techniques.
• Skopi provides a versatile platform for testing and refining XFEL data processing algorithms.

Conclusions:

• Skopi is a valuable resource for advancing noncrystalline XFEL experiments.
• It aids in the development and validation of new computational methods.
• The simulation package supports feasibility studies and experimental design for XFEL facilities.